Hi,
Is there any way in yt to get a script to delete (or ignore) all the .yt
and .harray files and clear its memory? I run into errors when I'm
re-doing a plot or I've re-run the simulation and over-written the last
data set I looked at with yt. I have to exit yt, delete the above files
by hand and restart, which is a bit of a pain.
Elizabeth

Hi Bretton, Matt,
All your advices came in handy, thank you very much! I already did some
trials with the files you (Matt) gave me, and they worked, now I'm doing
experiments on other simulations (with particles of course). Hopefully won't
be any issues.
Greetings

Hi everyone,
I've come across an error while trying to use yt for parallel analysis on Kraken. Wondering if its something people have seen before.
I have my simple script that does slices of a few different quanties. When I ran it with 12 tasks on Kraken, it worked fine for the first four datasets, but crashed during the fifth one. I tried a simpler script that just does a slice of density for that dataset, and it crashed again with the same error:
IndexError: arrays used as indices must be of integer (or boolean) type
When I ran this code again with only 1 task (still on Kraken, everything else the same), it worked fine. More of the output, as well as my job script and plotting script, are below.
Since it works in serial , and works for some data sets, the problem seems to be something to do with parallelism. Is there any sort of simple explanation or something I'm doing wrong?
Just wondering if this is something people have come across before.
--Greg
(Last few lines of output)
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File "/lustre/scratch/proj/sw/yt/current/lib/python2.7/site-packages/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/object_finding_mixin.py", line 69, in find_max_cell_location
File "/lustre/scratch/proj/sw/yt/current/lib/python2.7/site-packages/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/object_finding_mixin.py", line 69, in find_max_cell_location
File "/lustre/scratch/proj/sw/yt/current/lib/python2.7/site-packages/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/object_finding_mixin.py", line 69, in find_max_cell_location
max_grid = self.grids[mg]
IndexError: arrays used as indices must be of integer (or boolean) type
max_grid = self.grids[mg]
max_grid = self.grids[mg]
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
(Job script)
#!/bin/bash
#PBS -A TG-AST090040
#PBS -l size=12,walltime=2:00:00
#PBS -j oe
#PBS -N slicer
cd /lustre/scratch/oshea/nested_ics_real1/analysis
ls
pwd
export MPLCONFIGDIR=${PBS_O_WORKDIR}/.matplotlib/
[ ! -d ${MPLCONFIGDIR} ] && mkdir ${MPLCONFIGDIR}
module unload PrgEnv-pgi
module load PrgEnv-gnu
module load yt
aprun -n 12 python ./simple_slice.py --parallel
(simple_slice.py)
from yt.mods import *
DD = 40
fileName = "../DD%s/DD%s" % ((str(DD)).zfill(4), (str(DD)).zfill(4))
pf = load(fileName)
pc = PlotCollection(pf)
pc.add_slice("Density", 0)
pc.save("./%s" % str(DD).zfill(4))

Hi everyone,
I was making some projections using the YT module installed on Nautilus and encountered an odd issue: The projection is broken up and appears to be sort of tiled and jumbled around. You can see the result here: http://galactica.icer.msu.edu/~bcrosby/data/1024box/images/RedshiftOutput...
It looks similar to problems that arise from off-axis projections, but this projections are straight down the axis. I'm puzzled about what would be causing this, as the same script produced normal, smooth images earlier. Here's the plotting call that I used:
fn = "RD%04i/RedshiftOutput%04i" %(fnum,fnum)
pf = load(fn)
pc = PlotCollection(pf, center=[0.5,0.5,0.5])
for axis in range(3):
p = pc.add_projection("particle_density",axis)
Any clues as to what might be going on?
Thanks,
Brian

Hi Bretton,
After I put the command you gave me, this appears:
['0', '(do', 'not', 'modify')']
I guess the reason is what you said, but then I have another problem:
I can't find in the documentation any example I can use the HOP with;
there are examples of commands to use, but no one says what parameter file
are they using, if you can help I'd would be very grateful (I already am
actually).
Thank you.
Miguel

Hi,
I'm trying to install yt on the xt4 machine in Tokyo, which obnoxiously refuses to let you use wget.
I scp-ed a copy from my desktop to the xt4 and then told the install_script.sh where to find yt so it didn't try and download the packages. I also removed 'done' from each of the packages in src.
Unfortunately, I get:
gcc -fPIC -fPIC -o bzip2. bzip2.o -L. -lbz2
bzip2.o file not recognized: File format not recognized
xt4 does use modules for loading packages, but I don't know if I'm lacking a module or if my self-cleaning is flawed.
Elizabeth

Hi,
I was wondering if it is possible to specify two different sources of
input to create a derived field. Currently with a single source, I have a
derived field defined as:
def _HII_HFraction(field, data):
return data["HII_Density"]/(data["HI_Density"]+data["HII_Density"])
add_field("HII_HFraction", function=_HII_HFraction,
units=r"\frac{\rho_{HII}}{\rho_H}")
And I can access the total quantity in parallel
pf=load(file)
dd = pf.h.all_data()
dd.quantities["TotalQuantity"]("HII_HFraction")[0]
But I'm dealing with
pf1=load(file1)
pf2=load(file2)
pf1 has the HI_Density field data and pf2 has the HII_Density field data.
Is there a way to create a derived field and use TotalQuantity to operate
on the data in parallel?
From
G.S.
PS. I guess my alternative is to glue the two HDF5 files into one, but
want to avoid it if possible.